This is very odd that you have these duplicates ...
I would probably have to see your Zen Cart Admin, phpMyAdmin and have FTP access to go through things and see what is out of wack ...
This is not normal behavior for Zen Cart on the search and you should only see 1 of each product even when Linked to multiple categories on the search ...
Something is out of kilter here ... but there is a lot involved and quite a bit of work to determin the source of the problem ...
It could be the database tables, or the code, or an add-on or a file that is out of date ...
You might use something like Beyond Compare from scootersoftware.com to check your files on the server to see if they are all current and up to date or if there is an issue with something being old, changed, etc.
You can check all the database tables to see if you have something wrong with the:
products
products_description
categories
categories_description
products_to_categories
Or, you can always hire someone to go through and figure out what has really happened here ...
Without looking at these things I cannot estimate the time involved other than saying at least an hour to several ...